Dear Robbie,
In the case that only single monosaccharide was modelled at
glycosylation site with a known oligosaccharide sequence, technically
the software cannot generate glycosidic linkages, linear descriptors for
sequences, 2D SNFG images, etc. Therefore, this single monosaccharide
cannot be represented as a branched entity. However, if an author
provides PDB an updated coordinates with additional monosaccharides
modeled that bounds to the original monosaccharide, the software will
automatically detect this linkage and convert non-polymer entity of the
original monosaccharide into a branched entity (vice versa).
Regards,
Jasmine
===========================================================
Jasmine Young, Ph.D.
Biocuration Team Lead
RCSB Protein Data Bank
Research Professor
Institute for Quantitative Biomedicine
Rutgers, The State University of New Jersey
174 Frelinghuysen Rd
Piscataway, NJ 08854-8087
Email: jasm...@rcsb.rutgers.edu
Phone: (848)445-0103 ext 4920
Fax: (732)445-4320
===========================================================
On 12/9/20 4:35 AM, Robbie Joosten wrote:
Dear Jasmine,
I have a few questions about this bit:
//
As some users pointed out, single NAG could be just a part of the
glycan that the author chose to build, as most natural N-glycans must
have stem of a common core of 5 monosaccharides or its fucosylated
version, such as those modeled in the PDB ID 6WPS. However, the PDB is
a 3D-atomic coordinate archive in which the model coordinates are
built based on supporting experimental data. Therefore, carbohydrates
are described as-is in the modeled structures without reference to
missing components of the presumed oligosaccharide sequence. If the
author only builds a monosaccharide, then this monosaccharide is
described as a non-polymer ligand.
//
Is it technically allowed to have a single, covalently bound
carbohydrate described as a branched entity of length 1?
If so, if an author does specify such a single modeled residue as
branched entity, for instance because (s)he has a good reason to
suspect that a second residue was there, but isn’t comfortable with
building it, then is this specification kept in annotation?
If not, do you expect model building programs to switch from branched
to non-poly entities when a second residue is removed when a model is
written out? And back again when a residue is added? I find this
rather unpractical from an implementation point of view. We change
carbohydrate trees quite regularly.
Cheers,
Robbie
*From:*CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> *On Behalf Of
*Jasmine Young
*Sent:* Tuesday, December 8, 2020 21:01
*To:* CCP4BB@JISCMAIL.AC.UK
*Subject:* Re: [ccp4bb] Coming July 29: Improved Carbohydrate Data at
the PDB -- N-glycans are now separate chains if more than one residue
Dear PDB Data Users:
Thank you for providing feedback on the results of an archival-level
carbohydrate remediation project that led to the re-release of over
14,000 PDB structures in July 2020. This update includes diverse
oligosaccharides: glycosylation; metabolites such as maltose, sucrose,
cellulose fragments; glycosaminoglycans, such as fragments of heparin
and heparan sulfate; epitope patterns such as A/B blood group antigens
and the H-type or Lewis-type stems; and many artificial carbohydrates
mimicking or counting natural products
(https://www.wwpdb.org/documentation/carbohydrate-remediation
<https://www.wwpdb.org/documentation/carbohydrate-remediation>).
Starting in 2017, this PDB remediation aimed to standardize the
biochemical nomenclature of the carbohydrate components following the
IUPAC-IUBMB recommendations established by the carbohydrate community
(https://media.iupac.org/publications/pac/1996/pdf/6810x1919.pdf
<https://media.iupac.org/publications/pac/1996/pdf/6810x1919.pdf>),
and to provide uniform representation of oligosaccharides to improve
the identification and searchability of oligosaccharides modeled in
the PDB structures. During the remediation planning, wwPDB consulted
community users and the PDBx/mmCIF Working Group and made data files
available on GitHub in early 2020 for community feedback. wwPDB has
collaborated with Robert Woods at University of Georgia in US,
researchers at The Noguchi Institute and Soka University in Japan, and
Thomas Lutteke in Germany to generate uniform linear descriptors for
the oligosaccharide sequences.
To achieve these community goals, each oligosaccharide is represented
as a branched entity with complete biochemical description and each
glycosidic linkage specified. The full representation of carbohydrates
is provided in the mmCIF format file, but this is not possible in
legacy PDB format files (as the format has been frozen since 2012
(https://www.wwpdb.org/documentation/file-formats-and-the-pdb
<https://www.wwpdb.org/documentation/file-formats-and-the-pdb>).
Proper indexing is necessary for branched entity representation and
for generation of linear descriptors, hence the ordering (numbering)
starts at the reducing end (#1), where the glycosylation occurs, to
the non-reducing end in ascending order. Unique chain IDs are assigned
to branched entities (oligosaccharides) to avoid residue numbering
overlapped with protein residues and to enable consistent numbering
for every oligosaccharide. For example, in PDB ID 6WPS, there are 5
oligosaccharides associated with the same protein chain A, the
consistent ordering and numbering can only be retained with unique
chain ID for each oligosaccharide in both PDBx/mmCIF and PDB format files
For archival consistency, a single-monosaccharide is defined as a
non-polymer and treated consistently with other non-polymer ligands in
the PDB. A single-monosaccharide occurring at a glycosylation site has
a unique chain ID in the PDBx/mmCIF file (_atom_site.label_asym_id)
but not in the PDB format file.
Using PDB ID 6WPS as an example, the PDBx/mmCIF data item
_atom_site.label_asym_id corresponds to the column #7 in the atom_site
coordinates section has an asym ID ‘Y’ for the 1st instance of
single-monosaccharide, NAG bound to ASN 61 of protein chain ‘A’. The
‘Y’ value is unique for this monosaccharide. The additional chain ID
(_atom_site.auth_asym_id) in the PDBx/mmCIF file that mapped to the
PDB format file for this NAG is chain ‘A’, which is consistently
represented as any other non-polymer ligands associated with the
protein chain A.
#
loop_
_atom_site.group_PDB
_atom_site.id
_atom_site.type_symbol
_atom_site.label_atom_id
_atom_site.label_alt_id
_atom_site.label_comp_id
*_atom_site.label_asym_id*
_atom_site.label_entity_id
_atom_site.label_seq_id
_atom_site.pdbx_PDB_ins_code
_atom_site.Cartn_x
_atom_site.Cartn_y
_atom_site.Cartn_z
_atom_site.occupancy
_atom_site.B_iso_or_equiv
_atom_site.pdbx_formal_charge
_atom_site.auth_seq_id
_atom_site.auth_comp_id
*_atom_site.auth_asym_id*
_atom_site.auth_atom_id
_atom_site.pdbx_PDB_model_num
...
HETATM 27655 C C1 . NAG *Y* 6 . ? 191.103 162.375 206.665 1.00
47.28 ? 1301 NAG *A* C1 1
HETATM 27656 C C2 . NAG Y 6 . ? 191.067 161.665 208.065 1.00
47.22 ? 1301 NAG A C2 1
HETATM 27657 C C3 . NAG Y 6 . ? 190.138 160.434 207.960 1.00
47.42 ? 1301 NAG A C3 1
HETATM 27658 C C4 . NAG Y 6 . ? 188.730 160.906 207.541 1.00
48.73 ? 1301 NAG A C4 1
HETATM 27659 C C5 . NAG Y 6 . ? 188.838 161.622 206.176 1.00
48.66 ? 1301 NAG A C5 1
HETATM 27660 C C6 . NAG Y 6 . ? 187.494 162.153 205.709 1.00
48.17 ? 1301 NAG A C6 1
HETATM 27661 C C7 . NAG Y 6 . ? 193.233 161.885 209.217 1.00
47.40 ? 1301 NAG A C7 1
HETATM 27662 C C8 . NAG Y 6 . ? 194.594 161.311 209.471 1.00
47.45 ? 1301 NAG A C8 1
HETATM 27663 N N2 . NAG Y 6 . ? 192.418 161.218 208.414 1.00
47.36 ? 1301 NAG A N2 1
HETATM 27664 O O3 . NAG Y 6 . ? 190.069 159.774 209.231 1.00
47.22 ? 1301 NAG A O3 1
HETATM 27665 O O4 . NAG Y 6 . ? 187.867 159.778 207.435 1.00
48.89 ? 1301 NAG A O4 1
HETATM 27666 O O5 . NAG Y 6 . ? 189.760 162.757 206.285 1.00
47.83 ? 1301 NAG A O5 1
HETATM 27667 O O6 . NAG Y 6 . ? 186.953 163.102 206.622 1.00
49.06 ? 1301 NAG A O6 1
HETATM 27668 O O7 . NAG Y 6 . ? 192.879 162.950 209.739 1.00
47.58 ? 1301 NAG A O7 1
...
#
Author-provided chain ID and residue numbering for oligosaccharides
are retained in the PDBx/mmCIF file (_pdbx_branch_scheme.auth_mon_id
and _pdbx_branch_scheme.auth_seq_num, respectively). Users can map how
carbohydrates are described in the corresponding primary citation to
the PDBx/mmCIF files using _pdbx_branch_scheme mapping category. wwPDB
strongly encourages depositors to use the wwPDB-assigned chain ID and
residue numbers in any publication material.
For example, PDB entry 6WPS
#
loop_
*_pdbx_branch_scheme.asym_id *
_pdbx_branch_scheme.entity_id
_pdbx_branch_scheme.mon_id
_pdbx_branch_scheme.num
*_pdbx_branch_scheme.pdb_asym_id *
_pdbx_branch_scheme.pdb_mon_id
_pdbx_branch_scheme.pdb_seq_num
*_pdbx_branch_scheme.auth_asym_id *
_pdbx_branch_scheme.auth_mon_id
*_pdbx_branch_scheme.auth_seq_num*
_pdbx_branch_scheme.hetero
*J *4 NAG 1 *I* NAG 1 *A* NAG *1310* n
J 4 NAG 2 I NAG 2 A NAG 1311 n
K 4 NAG 1 J NAG 1 A NAG 1312 n
K 4 NAG 2 J NAG 2 A NAG 1313 n
L 4 NAG 1 K NAG 1 A NAG 1315 n
L 4 NAG 2 K NAG 2 A NAG 1316 n
M 4 NAG 1 M NAG 1 A NAG 1317 n
M 4 NAG 2 M NAG 2 A NAG 1318 n
N 5 NAG 1 N NAG 1 A NAG 1321 n
N 5 NAG 2 N NAG 2 A NAG 1322 n
N 5 BMA 3 N BMA 3 A BMA 1323 n
N 5 MAN 4 N MAN 4 A MAN 1325 n
N 5 MAN 5 N MAN 5 A MAN 1324 n
N 5 FUC 6 N FUC 6 A FUC 1320 n
O 4 NAG 1 O NAG 1 B NAG 1310 n
O 4 NAG 2 O NAG 2 B NAG 1311 n
P 4 NAG 1 P NAG 1 B NAG 1312 n
P 4 NAG 2 P NAG 2 B NAG 1313 n
Q 4 NAG 1 Q NAG 1 B NAG 1315 n
Q 4 NAG 2 Q NAG 2 B NAG 1316 n
R 4 NAG 1 R NAG 1 B NAG 1317 n
R 4 NAG 2 R NAG 2 B NAG 1318 n
S 5 NAG 1 S NAG 1 B NAG 1321 n
S 5 NAG 2 S NAG 2 B NAG 1322 n
S 5 BMA 3 S BMA 3 B BMA 1323 n
S 5 MAN 4 S MAN 4 B MAN 1325 n
S 5 MAN 5 S MAN 5 B MAN 1324 n
S 5 FUC 6 S FUC 6 B FUC 1320 n
...
#
As some users pointed out, single NAG could be just a part of the
glycan that the author chose to build, as most natural N-glycans must
have stem of a common core of 5 monosaccharides or its fucosylated
version, such as those modeled in the PDB ID 6WPS. However, the PDB is
a 3D-atomic coordinate archive in which the model coordinates are
built based on supporting experimental data. Therefore, carbohydrates
are described as-is in the modeled structures without reference to
missing components of the presumed oligosaccharide sequence. If the
author only builds a monosaccharide, then this monosaccharide is
described as a non-polymer ligand.
Glycosylation annotation has been provided to facilitate searches of
all glycosylation sites. A total of 45,000 glycosylation sites have
been annotated in _struct_conn.pdbx_role in over 7500 PDB structures
to identify all glycosylation sites and the monosaccharides bound at
such sites. The annotation specifies the glycosylation sites, the
monosaccharide identity and chain IDs in either PDB format or mmCIF
format. In PDB ID 6WPS, a user can search N-Glycosylation in
‘_struct_conn.pdbx_role’ and find 16 glycosylation sites between ASN
and NAG at chain A alone.
The wwPDB encourages the community to use PDB/mmCIF format files
rather than the frozen legacy PDB file format. The legacy format
cannot support large structures. Currently, PDB format-files are not
available for large structures that have either more than 62 chains or
99,999 atoms. In addition, the legacy format cannot support ligand ID
codes beyond 3-characters, which will be needed in the coming years.
We thank you again for your feedback. The wwPDB is committed to
improving data representation in the PDB archive. Please do not
hesitate to contact us at i...@wwpdb.org <mailto:i...@wwpdb.org>.
Regards,
Jasmine
===========================================================
Jasmine Young, Ph.D.
Biocuration Team Lead
RCSB Protein Data Bank
Research Professor
Institute for Quantitative Biomedicine
Rutgers, The State University of New Jersey
174 Frelinghuysen Rd
Piscataway, NJ 08854-8087
Email:jasm...@rcsb.rutgers.edu <mailto:jasm...@rcsb.rutgers.edu>
Phone: (848)445-0103 ext 4920
Fax: (732)445-4320
===========================================================
On 12/4/20 3:15 PM, Marcin Wojdyr wrote:
On Fri, 4 Dec 2020 at 19:16, Dale Tronrud<de...@daletronrud.com>
<mailto:de...@daletronrud.com> wrote:
Creating meaning in the chain names "A, B, C, Ag1, Ag2, Ag3" is
exactly the problem.
It's not about "creating meaning" but about consistent naming. For humans.
"chain names" ( or "entity identifiers" if I
recall the mmCIF terminology correctly) are simply database "indexes".
No, entity is a somewhat different thing (multiple chains can point to
the same entity). entity_id is specified in addition to label_asym_id
and auth_asym_id.
asym = "structural element in the asymmetric unit" (so-called chain).
The values of indices are meaningless in themselves, they are just
unique values that can be used to unambiguously identify a record. In
principle, you could just assign random ISO characters (I don't think
mmCIF allows unicode) and the mmCIF would be considered identical.
And then you'd use this random string also in a publication when
referring to the chain, and in the user interface?
You are trying to force meaning to the characters with an index,
and
that puts multiple types of information in a single field. As Robbie
said already exists, if you want to encode connectivity into the data
base you have to add records that define that connectivity. That places
the connectivity information explicitly in the data models and allows
standard data base tools to track and validate.
No one was proposing to replace connectivity with names.
It was about naming that will be easier to work with for people.
learn the sequence you have to go to the mmCIF records that define the
connectivity between residues. It is entirely possible that "3" comes
before "1" because these indexes don't contain any information, other
than being unique within the chain.
In mmCIF you have label_seq_id that must be both unique and
sequential. So 3 is always the third residue wrt to the full sequence.
########################################################################
To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
<https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1>
This message was issued to members ofwww.jiscmail.ac.uk/CCP4BB
<http://www.jiscmail.ac.uk/CCP4BB>, a mailing list hosted bywww.jiscmail.ac.uk
<http://www.jiscmail.ac.uk>, terms & conditions are available
athttps://www.jiscmail.ac.uk/policyandsecurity/ <https://www.jiscmail.ac.uk/policyandsecurity/>
------------------------------------------------------------------------
To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
<https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1>
-->
########################################################################
To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list
hosted by www.jiscmail.ac.uk, terms & conditions are available at
https://www.jiscmail.ac.uk/policyandsecurity/
